- Pelaez-Rodríguez, E., J. Franco-López, W. A. Matamoros, R. Chavez- López, and N. J. Brown-Peterson. 2005. Trophic relationships of demersal fishes in the shrimping zone off Alvarado Lagoon, Veracruz, Mexico. Gulf and Caribbean Research 17:157-167.
- Matamoros, W. A., K. D. Chin, and B. Sharfstein. 2005. First report of the Mayan Cichlid, Cichlasoma urophthalmus (Günther 1862) collected in the southern littoral zone of Lake Okeechobee, Florida. Gulf and Caribbean Research 17:113-115.
- Schaefer, J.F., Mickle, P., Spaeth, J., Zuber, B., Matamoros, W., Adams, S., Kreiser, B., Vigueira, P. 2006. Effects of Hurricane Katrina on the fish fauna of the Pascagoula drainage. Proceedings of the Mississippi Water Resources Board 36:62-68.
- Jaime García-Moreno , Amy Upgren , Jorge Iván Restrepo , Wilfredo Matamoros , Alfredo D. Cuarón , Topiltzin Contreras-MacBeath , Nora López , John Lamoreux , Meghan McKnight , Antonio Muñoz , Paul Walker, Josiah Townsend , Carlos Vásquez-Almazán , Claudia Macías , Oliver Komar , Jim Barborak , Ruth Jiménez y Jaime R. Bonilla-Barbosa. 2008. Los sitios mas críticos para evitar extinciones de especies globalmente amenazadas: la importancia de su identificación y de recabar información del el campo. Mesoamericana 11: 59-63.
- Matamoros, W. A., J. F. Schaefer, P. Mickle, W. Arthurs, J. Ikoma, and R. Ragsdale. 2009. First Record of Agonostomus monticola (Family: Mugilidae) in Mississippi freshwaters with notes of its distribution in the Southern USA. Southeastern Naturalist. 8: 175-178.
- Feldheim, K. A., P. J. Sanchez, W. A. Matamoros, J. Schaefer, and B. Kreiser. 2009. Isolation and characterization of microsatellite loci for Mountain Mullet (Agonostomus monticola). Molecular Ecology Resources. 9: 1482-1484.
- Matamoros, W. A., J. Schaefer and B. Kreiser. 2009. Annotated systematic checklist of the continental and island fishes that occur in Honduran freshwaters. Zootaxa. 2307: 1-38
- McMahan Caleb D., Wilfredo A. Matamoros, Francisco S. Alvarez Calderon, Wendy Henriquez, H. Michelle Recinos, Prosanta Chakrabarty, Enrique Barraza, & Nestor Herrera. 2013. Checklist of the Inland Fishes of El Salvador. ZOOTAXA. 3608: 440–456.
- Matamoros W. A., P. Chakrabarty, A. Angulo-Sibaja, C.A. Garita-Alvarado, and C.D. McMahan. 2013. A new species of Roeboides (Teleostei: Characidae) from Costa Rica and Panama, with a key to all Middle American species. Neotropical Ichthyology. 11: 285-290.
- Bohn Sandra, Enrique Barraza, Caleb McMaham, Wilfredo A. Matamoros & Brian Kreiser. 2013. Cross amplification of microsatellite loci developed for alligator gar (Atractosteus spatula) in tropical gar (Atractosteus tropicus). Revista Mexicana de Biodiversidad. 84:1349-1351.
- Elizabeth Harrison, Joel C. Trexler, Timothy M. Collins, Ella Vazquez, Ulises Razo-Mendivil, Wilfredo A. Matamoros, and Christian Barrientos. 2014. Genetic evidence for multiple sources of the non-native fish Cichlasoma urophthalmus (Mayan Cichlids) in southern Florida. In press: Plos One. 9(9), e104173.
- Caleb D. McMahan, Wilfredo A. Matamoros, Justin Kutz and Prosanta Chakrabarty. 2014. Taxonomic status of Amatitlania coatepeque (Teleostei: Cichlidae). COPEIA. 2014(4) 633-638.
- Guillermo Salgado-Maldonado, Wilfredo A. Matamoros, Juan Manuel Caspeta-Mandujano, Emilio Martínez-Ramírez, Edgar F. Mendoza-Franco and Ernesto Velázquez-Velázquez. 2014. Range extension of helminth parasites of Profundulus spp. (Teleostei: Profundulidae) from Southern Mexico and Central America. Check List. 10: 1507-1513.
- Matamoros Wilfredo A., Caleb D. McMaham, Prosanta Chakrabarty, James S. Albert and Jacob F. Schaefer. 2015. Derivation of the Freshwater Fish Fauna of Central America Revisited: Myers’s hypothesis in the 21st Century. CLADISTICS. 31: 177-188.
- Guillermo Salgado-Maldonado, Wilfredo A. Matamoros, Brian R. Kreiser, Juan Manuel Caspeta-Mandujano, and Edgar F. Mendoza-Franco. 2015. First record of the invasive Asian fish tapeworm Bothriocephalus acheilognathi in Honduras, Central America. Parasite . 22: 1-6.
- Ernesto Velázquez-Velázquez, Betsabe Mendez-Gómez, Guillermo Salgado-Maldonado and Wilfredo Matamoros. 2015. The invasive tapeworm Bothriocephalus acheilognathi Yamaguti, 1934 in the endangered killifish Profundulus candalarius Hubbs, 1924 in Chiapas, Mexico. BioInvasions Records. 4: 265–268 .
- Caleb D. McMahan, Wilfredo A. Matamoros, Kyle R. Piller & Prosanta Chakrabarty. 2015. Taxonomy and systematics of the herichthyins (Cichlidae: Tribe Heroini), with the description of eight new Middle American Genera. ZOOTAXA. 3999 (2): 211–234 .
- Matamoros, W. A., Hoagstrom, C. W., Schaefer, J. F., & Kreiser, B. R. 2015. Fish faunal provinces of the conterminous United States of America reflect historical geography and familial composition. Biological Reviews. 91. 813–832. .
- Tagliacollo, V. A., Duke-Sylvester, S. M., Matamoros, W. A., Chakrabarty, P., & Albert, J. S. (2015). Coordinated Dispersal and Pre-Isthmian Assembly of the Central American Ichthyofauna. Systematic biology, syv064.
- Edgar F. Mendoza-Franco, Juan Manuel Caspeta-Mandujano, Guillermo Salgado-Maldonado and Wilfredo Antonio Matamoros. 2015. Two new species of Urocleidoides Mizelle et Price, 1964 (Monogenoidea) from the gill lamellae of profundulids and poeciliids from Central America and southern Mexico. 62: 095.
- Morcillo, F., Ornelas-García, C. P., Alcaraz, L., Matamoros, W. A., & Doadrio, I. 2016. Phylogenetic relationships and evolutionary history of the Mesoamerican endemic freshwater fish family Profundulidae (Cyprinodontiformes: Actinopterygii). Molecular Phylogenetics and Evolution, 94, 242-251.
- Ennen, J., Agha, M., Matamoros, W., Hazzard, S., & Lovich, J. E. 2016. Using climate, energy, and spatial-based hypotheses to interpret macroecological patterns of North America chelonians. Canadian Journal of Zoology, (ja).
- Matamoros, W. A., McMahan, C. D., Mejia, C. R., House, P. H., Armbruster, J. W., & Chakrabarty, P. 2016. First record of the non-native sukermouth armored catfish Hypostomus cf. niceforoi (Fowler 1943) (Siluriformes: Loricariidae) from Central America.
- Bagley, J. C., Matamoros, W. A., McMahan, C. D., Tobler, M., Chakrabarty, P., & Johnson, J. B. 2016. Phylogeography and species delimitation in convict cichlids (Cichlidae: Amatitlania): implications for taxonomy and Plio–Pleistocene evolutionary history in Central America. Biological Journal of the Linnean Society.
- Jamangape, A., Velázquez-Velázquez, E., Martínez-Ramirez, E., Anzueto-Calvo, M. J., Gomez, E. L., Dominguez-Cisneros, S. E., McMahan, C. D., & Matamoros, W. A. 2016. Validity and Redescription of Profundulus balsanus Ahl, 1935 (Cyprinodontiformes: Profundulidae). Zootaxa, 4173(1), 55-65.
- Velázquez-Velázquez, E., Jesús Manuel López-Vila, Adán Enrique Gómez-González, Emilio Ismael Romero-Berny, Jorge Luis Lievano-Trujillo, Wilfredo A. Matamoros. 2016. A checklist and distribution of the inland waters fishes of the state of Chiapas, Mexico. ZOOKEYS.